I agree that atheists are likely much less certain about their answers to ultimate philosophical or cosmological questions. That doesn't change the limitations of their possible answers.

The psychological question of certainty is different from the metaphysical one of what could possibly be ultimate for atheists. Atheistic naturalists are stuck with a monstrous form of pantheism, as far as I can tell. There would have to be an eternal bottom of nature, a self-levitating turtle to support all the other turtles, or naturalistic explanations would have to be endless, as I argue elsewhere. Either scenario is roughly as preposterous as theism, for different reasons. Reason ends at the point at which preposterousness begins.

I have another article I've recently written that takes up this quesiton of the atheist's First Cause, or rather the source of the laws of nature, based on an exchange between Paul Davies and some other scientists.